Neisseria meningitidis is a major cause of bacterial meningitis. Strains of N. meningitidis express one of two porin proteins. These proteins have been identified as the class 2 and class 3 proteins, and express serotype specific epitopes. They have been evaluated as vaccine constituents. We obtained the gene for the class 3 proteins, and express serotype specific epitopes. They have been evaluated as vaccine constituents. We obtained the gene for the class 3 protein by PCR from a serotype 4 strain as a 1,025 bp fragment. The sequence of this gene was obtained and compared to two recently published sequences. Based upon this comparison we identified two possible variable regions that may be associated with serotype specificity. Primers were prepared to obtain sequences in the VR1 and VR2 regions from 5 additional group B N. meningitidis strains of serotypes 1, 4, 8, 12 and 15, all expressing class 3 proteins. The VR1 and VR2 regions were hypervariable and flanked by highly conserved regions among eight different class 3 sequences. These two hypervariable regions of 15 and 9 amino acids are predicted to be in surface exposed loops.